Compositions and Methods for Stabilizing Circulating Tumor Cells

ABSTRACT

Compositions and Methods for Stabilizing Circulating Tumor Cells Methods and compositions for stabilizing a biological sample for analysis, comprising the steps of obtaining in a sample collection device a biological sample from a subject, especially blood, the biological sample including at least one circulating tumor cell from the subject. The methods may include a step of contacting the biological sample with a protective agent composition that includes a preservative agent, an optional anticoagulant, and a quenching agent to form a mixture that includes the protective agent composition and the sample.

FIELD OF THE INVENTION

The teachings herein relate to devices and methods for stabilizing and preserving circulating tumor cells without damaging the tumor cell integrity for improved protection and regulation of circulating tumor cells during collection, storage, and shipment.

BACKGROUND OF THE INVENTION

In the peripheral blood of patients with solid tumors of epithelial origin, studies have identified circulating cells that have characteristics of tumor cells. These cells that are present in the bloodstream of cancer patients (referred to as circulating tumor cells or CTCs) are thought to play an important role in cancer metastasis by breaking loose from a solid tumor, entering the circulation, and then migrating to distant organs to develop secondary tumors. As such, circulating tumor cell (CTC) enumeration and characterization in the blood of cancer patients is useful for cancer prognostic and treatment monitoring purposes. Even though the number of CTCs present in patient blood is very low, robust technologies have been developed to enumerate and characterize CTCs in patient blood samples. CTCs are detectable in the blood of patients with metastatic cancer using a number of different technologies. Since CTCs are rare they need to be enriched from patient blood for accurate enumeration and characterization. Most of the CTC enrichment and identification assays available today are based on enrichment with anti-EpCAM antibodies and subsequent identification using anti-cytokeratin antibodies. An example is the CellSearch® instrument system available from Janssen Diagnostics, Raritan, N.J.

While the presence of CTCs in patients with cancer has been known for over a century, utilization of these rare cells in cancer diagnosis and prognosis was not feasible since methodologies to detect, isolate and characterize CTCs have not been developed until recently. With the development of robust methodologies to enrich, isolate and characterize CTCs in different types of cancers that are found in solid organs, several clinical studies have been conducted to investigate the possible use of CTCs in cancer diagnosis and prognosis. Assays that enumerate CTCs using the Cell Search® system have been developed for use as an aid to monitor patients with metastatic breast, colorectal, and prostate cancers. It has also been shown the potential usefulness of CTC enumeration using the Cell Search™ system for monitoring patients with melanoma, urothelial, and lung cancer.

Factors that limit the utility of CTCs in cancer diagnosis and prognosis are the low abundance and the fragility of the CTCs that may introduce variability in the evaluation of CTCs using different assay platforms, Transportation of blood samples from the site of phlebotomy to another facility is commonly required for CTC enumeration and characterization. During post-phlebotomy blood sample transportation/storage, fragile CTCs may degrade and compromise the accuracy of CTC enumeration and characterization.

There is a growing interest in the use of CTCs in non-invasive diagnosis, prognosis and monitoring of treatment regimens. The low abundance of the CTCs and their fragile nature may introduce variability in the evaluation of CTCs using different assay platforms. This fragile nature of CTCs arises due to the apoptosis of CTCs which begins after separation from the tumor of origin and after removal of blood from a patient. Therefore, it is necessary to address several pre-analytical issues that arise during the time between blood draw and CTC enrichment and characterization in order to effectively preserve the CTCs for analysis. These include delays in blood processing, blood storage temperature, and agitation of the sample during transport and shipment of blood. Such conditions may affect the integrity of already fragile CTCs causing accurate enumeration and characterization of CTCs difficult. As a result, it is important to consider the type of blood collection device and post-phlebotomy conditions while working with CTC samples.

There is thus a need for methods of stabilizing and protecting circulating tumor cells whereby structural integrity is maintained so that shipping and storage is possible with minimal deleterious effect on the circulating tumor cells. There is a further need for such methods where the detrimental effects of aldehyde fixation are avoided.

SUMMARY OF THE INVENTION

The teachings herein employ a protocol using a unique protective agent composition that successfully preserves samples while stabilizing CTC integrity for a prolonged period (e.g., which may be at least 14 days, and which may be at room temperature). The present teachings provide a consistent and efficient method for preserving CTCs in biological samples. Data demonstrated herein describes a method that reduces cell lysis and nuclease activity, and also permits accurate and precise analytical analysis by virtue of the preservation of the final concentration of recoverable CTCs over time. In so doing, the teachings provide a novel approach that improves the downstream clinical analysis of CTCs. The present teachings describe protecting the CTCs by inhibiting all cellular metabolic activity in CTCs in blood. As a result of metabolic inhibition of CTCs in blood all apoptotic and necrotic pathways are inhibited and CTCs are protected from cell degradation. Therefore it is no longer necessary to isolate and characterize CTCs immediately after venipuncture. Furthermore, samples can be stored at room temperature for up to 14 days without deleterious effects to sample integrity, which eliminates the need for cold storage of the blood sample,

In one aspect, the present teachings contemplate a method for blood sample treatment comprising locating a protective agent into the blood collection devices described herein. The protective agent may include a preservative. A blood sample may be drawn into the blood collection device, the blood sample having a first CTC concentration. The blood collection device containing a blood sample may be transported from a first location to a second location, wherein at least a portion of the transporting occurs at a temperature of greater than about 0° C. The CTCs from the sample may be isolated at least 24 hours after blood draw, the sample having a second CTC concentration, wherein the second CTC concentration is not lower or higher than the first CTC concentration by any statistically significant value.

The teachings herein further include that the preservative may be selected from the group consisting of diazolidinyl urea and imidazolidinyl urea. The concentration of the preservative prior to the contacting step may be between about 0.1 g/ml and about 3 g/ml. The circulating tumor cells may be isolated from the sample at least 3 days after blood draw. The circulating tumor cells may be isolated from the sample at least 7 days after blood draw. The circulating tumor cells may be isolated from the sample at least 14 days after blood draw. The transporting step may occur without freezing the blood sample to a temperature colder than about −30° C. The protective agent may contact the circulating tumor cells so that after a period of at least 7 days from the time the blood sample is drawn, the amount of circulating tumor cells is at least about 90% of the amount of circulating tumor cells at the time the blood sample is drawn. The protective agent may contact the circulating tumor cells so that after a period of at least 7 days from the time the blood sample is drawn, the amount of circulating tumor cells present in the sample is about 100% of the amount of circulating tumor cells present in the sample at the time the blood sample is drawn,

The teachings herein contemplate improved protective agent compositions, and methods of stabilizing a biological sample for analysis. The protective agent compositions will generally include a preservative agent as described herein, and a quenching agent for substantially abating any free aldehyde (e.g., formaldehyde) from reacting with DNA within a sample. The protective agent composition may also include one or more nuclease inhibitors. The protective agent composition may also include one or more metabolic inhibitors. The methods described herein may comprise a step of obtaining in blood collection device a biological sample from a subject. The biological sample may include at least one circulating tumor cell from the subject. The methods may include a step of contacting the biological sample while within the blood collection device with a protective agent composition that includes a preservative agent, an optional anticoagulant, and a quenching agent to form a mixture that includes the protective agent composition and the sample. The methods may include a step of quenching any free formaldehyde that may be present with the quenching agent from the protective agent composition so that the free formaldehyde reacts to form a reaction product that is inert to the CTCs within the biological sample. The resulting mixture may be devoid of any aldehyde, and CTCs within the sample may be suitable for downstream applications.

For samples derived from blood, there may be a blood draw step of drawing blood from a patient into a blood collection device that has the protective agent composition loaded therein prior to the blood draw step. The method may include a step of transporting the sample while it is contacted with the protective agent composition from a blood draw site to a clinical laboratory (e.g., one located at least 100 meters, 1000 meters, 10,000 meters from the blood draw site) at which a sample analysis will occur. The quenching occurs prior to and/or substantially simultaneously with the contacting step. The methods may include a step of isolating circulating tumor cells from the sample. The methods may be free of any step of centrifugation of the sample. The methods may be free of any step of isolating cell-free fetal DNA, cell-free DNA, cell-free RNA or cellular RNA from a blood sample. The methods may be free of any step of refrigerating the sample (e.g., to a temperature below room temperature, such as about 10° C. or cooler) after it has been contacted with the protective agent composition.

As can be appreciated from the above, the teachings herein provide for advantageous treatment of CTC-containing samples and provide stabilized samples that are essentially free of detectable covalent modifications that inhibit downstream testing of the characteristics of CTCs.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a graph displaying the effect of two exemplary protective agent compositions and a standard K₃EDTA composition on MCF-7 cell recovery at Day 1 and Day 4 post blood draw.

FIG. 2 shows immunofluorescence cell staining results (EpCAM and Cytokeratin) of two exemplary protective agent compositions and a standard K₃EDTA composition.

FIG. 3 shows fluorescence cell staining results showing levels of mRNA expression after contact with one exemplary protective agent composition and a standard K₃EDTA composition.

DETAILED DESCRIPTION

This application is related to and claims the benefit of the filing date of U.S. Provisional Application Ser. No. 61/857,847 filed Jul. 24, 2013, the contents of this application being hereby incorporated by reference for all purposes.

The explanations and illustrations presented herein are intended to acquaint others skilled in the art with the teachings, its principles, and its practical application. Those skilled in the art may adapt and apply the teachings in its numerous forms, as may be best suited to the requirements of a particular use. Accordingly, the specific embodiments of the present teachings as set forth are not intended as being exhaustive or limiting of the teachings. The scope of the teachings should, therefore, be determined not with reference to the above description, but should instead be determined with reference to the appended claims, along with the full scope of equivalents to which such claims are entitled. The disclosures of all articles and references, including patent applications and publications, are incorporated by reference for all purposes. Other combinations are also possible as will be gleaned from the following claims, which are also hereby incorporated by reference into this written description.

Unless otherwise stated, percentages as set forth herein refer to percent by weight. Further, unless the context of the discussion makes dear to the contrary, references to circulating tumor cells refers not only to intact circulating tumor cells, but to tumor cell fragments.

The present teachings contemplate a non-invasive screening method for the identification of circulating tumor cells that are potentially indicative of cancer diagnosis and progression. The teachings herein envision not only preserving the state of any cells in a sample but also envisions protecting the circulating tumor cells from any adverse effects during any delay between sample collection and processing and/or testing. The methods of the teachings herein generally involve steps of contacting a biological sample (which may include multiple blood cells and cell-free biomolecules), with an aldehyde-free (e.g., formaldehyde-free) protective agent composition in an amount and time that is sufficient to prevent degradation of the circulating tumor cells. The treatment is such that it substantially prevents any free aldehyde from adversely reacting with the CTCs of the sample such as by employing a quenching agent. In this manner, substantial quantities of CTCs can be maintained within and isolated from the sample. The CTC integrity is substantially preserved in its as provided state (e.g., the state at the time of blood draw) by avoiding the damaging effects of any aldehyde (e.g., formaldehyde). Thus, accurate and precise analytical analysis of the CTCs of the sample can be achieved. The method may further include steps of analyzing the CTCs from a sample that has been treated in accordance with the above, or that have otherwise been contacted with the protective agent composition and the quenching agent therein. As noted, the teachings herein permit identification of CTC characteristics for prognostic and diagnostic use of various pathological conditions in the clinic.

Protective Agent Compositions A & B as described in the examples below and shown in the drawings include a formaldehyde free stabilization reagent that stabilizes CTCs in a blood sample for up to 14 days at room temperature. They do so by inhibiting cell metabolism in CTCs in blood and preventing cellular apoptosis and necrosis that degrade the CTCs in blood These examples were designed to investigate the effectiveness of this blood collection devices for the stabilization of CTCs in a blood sample for an extended period of time at room temperature.

The study was approved by the institutional review board of the Methodist Hospital, Omaha, Nebr., USA and informed consent was obtained from all donors prior to blood draw. Blood specimens were collected from apparently healthy adult donors by standard phlebotomy techniques.

Breast cancer cell line, MCF-7 cells was obtained from American Type Culture Collection (Rockville, Md., USA) and routinely passaged in Eagle's MEM medium containing 10% fetal bovine serum at 37° C. in humidified atmosphere of 5% CO₂.

For the MCF-7 cell spiking experiment, blood from each healthy donor (7 donors in total) was drawn into 10 mL K₃EDTA tubes (BD Vacutainer®, Becton Dickinson, Franklin Lakes, N.J., USA), and 10 mL tubes containing Protective Agent A and 10 mL tubes containing Protective Agent B. The blood volume was as close to 10 mL as possible for all tube types. MCF-7 cells (2000 cells/10 mL blood) were then spiked into all tubes and blood was mixed immediately after spiking by inverting 10 times each. All samples were shipped at ambient temperature to Geneuity Clinical Research Services (Maryville, Tenn., USA) and analyzed on the CellSearch system on days 1 and 4 post phlebotomy to determine the stability of spiked MCF-7 cells. Blood samples were maintained at room temperature during the entire process.

While the CellSearch system was utilized for the examples herein, it is envisioned that the protective agent compositions described herein could be utilized with any device and/or platform equipped for tumor cell enrichment and characterization,

EXAMPLES

Blood was drawn from each donor into multiple 10 mL K₃EDTA tubes and multiple 10 mL tubes for each of Protective Agent. Compositions A & B. All tube types were spiked with MCF-7 breast cancer cells and stored at room temperature, Spiked MCF-7 cells were enumerated using the CellSearch™ system on days 1 and 4. Effect of storage on the stability of proteins and nucleic acids in MCF-7 cells isolated from K₂EDTA tube and Protective Agent Compositions A & B was determined using fluorescent staining and confocal laser scanning microscopy.

Overall, enumeration of MCF-7 cells in K₂EDTA blood showed a significant drop in recovered MCF-7 cells at day 1 and 4 compared to values obtained for Protective Agent Compositions A & B. However, in blood drawn into tubes containing Protective Agent Compositions A & B, MCF-7 cell count was stable up to 4 days at room temperature. Epithelial cell adhesion molecule (EpCAM) and cytokeratin (CK) in MCF-7 cells isolated from tubes containing Protective Agent Compositions A & B were stable at room temperature for up to 4 days, whereas in MCF-7 cells isolated from K₃EDTA blood showed reduced EpCAM and CK protein expression. The CK protein expression showed no significant change over 4 days in tubes containing Protective Agent Compositions A & B. Similarly, Protective Agent Composition A showed improved stabilizing of c-fos mRNA as compared to K₃EDTA tubes. No significant change in cyclin D1 mRNA expression was observed in all tubes.

As further discussed in the details below, Protective Agent Compositions A & B provide preservation and stabilization of CTCs in blood samples for at least 4 days at room temperature. In doing so, it facilitates the development of new non-invasive diagnostic and prognostic methodologies for CTC enumeration as well as characterization.

Effect of storage on the stability of EpCAM and CK determined by immunofluorescence cell staining—FIG. 2

Blood was drawn from each donor into one 10 mL K₃EDTA tube, one 10 mL tube containing Protective Agent Composition A, and one 10 mL tube containing Protective Agent Composition B. Plasma was separated from blood within 2 h post collection. To separate plasma, blood samples were centrifuged at 300×g for 20 min at room temperature. The upper plasma layer was carefully removed without disturbing the buffy coat and transferred to a new tube that was then centrifuged at 5000×g for 10 min. The cell-free plasma was then spiked with MCF-7 cells 2,000 cells /4-5 mL of plasma) and stored at room temperature, On days 0 and 4, MCF-7 cells were washed with phosphate buffered saline solution and centrifuged at 500 rpm for 7 minutes on glass slides using Shandon Cytospie 3 cytocentrifuge. Slides were then dried and immunostaining for EpCAM and Cytokeratin were carried out with a primary antibody cocktail containing a mouse anti-EpCAM antibody (VU-1D9, #sc-51681 , 1:1:100) and a mouse anti-CK antibody (T-13, #sc-241376, 1:100). After 1 h of incubation, slides were washed twice with PBS and probed with fluorescent labeled secondary antibodies for mouse anti-EpCAM (donkey anti-mouse IgG-FITC, #sc-2099, 1:200) and mouse anti-CK (donkey anti-goat IgG-PerCP-Cy5.5, #sc-45102, 1:200) antibodies for 1 h. After washing slides twice with PBS, coverslips were mounted onto slides with UltraCruz™ mounting medium (#sc-24941) containing 4′, 6-diamidino-2-phenylindole (DAPI) to counterstain cell nuclei. All antibodies and mounting medium were purchased from Santa Cruz Biotechnology, Inc. (Dallas, Tex., USA) and manufacturer's protocol was followed. Fluorescent images were obtained using Zeiss LSM 510 META NLO laser scanning confocal microscope (Oberkochen, Germany).

Effect of storage on the stability of mRNA molecules using molecular beacons—FIG. 3

Cytospin slides of spiked MCF-7 cells were prepared as described above. Cells on the slides were treated with ice cold methanol (−10° C.) for 5 to 10 min. After air drying, the slides were stained with a mixture of 200 nmol/L of fluorescent-tagged molecular beacons targeting c-fos or cyclin D1 mRNAs in Opti-MEM (Invitrogen) at 37° C. for 1 h. Stained cells on the slides were then washed, counterstained with DAPI and examined using a confocal microscope. The molecular beacons were purchased from Eurofins MWG Operon (Fluntsviile, Ala.).

Stability of spiked MCF-7 cells in blood—FIG. 1

Experiments were carried out to determine the ability of Protective Agent Compositions A & B to stabilize CTCs during blood sample storage and transportation as compared to regular K₃EDTA blood collection tubes. Parallel blood samples drawn into K₃EDTA and tubes containing Protective Agent Compositions A & B and spiked with MCF-7 cells were analyzed using the CellSearch system for spiked tumor cell recovery. As shown in FIG. 1 , Protective Agent Compositions A & B demonstrated desired percentage recovery of the tumor cells at room temperature for up to 4 days. In Protective Agent Compositions A & B, at day 1, 60% (Standard deviation (SD)=4%, coefficient of variation (CV)=7.3%) of spiked MCF-7 cells were recovered and at day 4 it was 58% (SD=8%, CV=14.3%). In contrast, K₃EDTA tubes failed to preserve CTCs resulting in a much lower recovery rates for both day 1 and 4 as compared to Protective Agent Compositions A & B. In K₃EDTA tubes, at day 1, recovery rate was 32% (SD=12%, CV=36.3%) of the spiked MCF-7 cells and at day 4 it was 16% (SD=14%, CV=87%).

Effect of storage on the stability of EpCAM and CK proteins determined by immune fluorescence cell staining—FIG. 2

FIG. 2 illustrates the effects of room temperature storage on the stability of tumor-associated transmembrane protein EpCAM and cytoskeleton protein cytokeratin of MCF-7 tumor cells spiked into blood plasma. According to FIG. 2 , EpCAM protein which is expressed on the cell membrane of MCF-7 cells are stable up to 4 days at, room temperature in tubes containing Protective Agent Compositions A & B whereas in K₃EDTA tubes this membrane protein was partially degraded by day 4. According to FIG. 2 , fluorescence signal for EpCAM cell membrane protein is very weak and diffused in MCF-7 cells spiked into K₃EDTA blood at day 4, CK protein is stabilized in tubes containing Protective Agent Compositions A & B at day 4, however this protein was less stable in K₃EDTA tubes at day 4 as evidenced from reduced fluorescence intensity for this protein in spiked MCF-7 cells recovered from K₃EDTA tubes. Staining of cells with DAPI shows that nucleus and nuclear content is stable in cells recovered from tubes containing Protective Agent. Compositions A & B but not from cells recovered from K₃EDTA tubes after 4 days of storage at room temperature (FIG. 2 ).

Effect of storage on the stability of mRNA molecules using molecular beacons—FIG. 3

Experiments were carried out to study the stability of mRNA in spiked MCF-7 cells recovered from Protective Agent Composition A and K₃-EDTA tubes. Cytospins of recovered MCF-7 cells were prepared as described above. To detect mRNA in situ, fluorescent-labeled molecular beacons and a scanning confocal microscope was used. As shown in FIG. 3 , c-fos mRNA (green fluorescence) and cyclin D1 mRNA (red fluorescence) were both stable in Protective Agent Composition A up to 4 days at room temperature. However in K₃EDTA tubes c-fos mRNA was not stable after 4 days of storage at room temperature, indicating that c-fos mRNA expression was significantly degraded or downregulated. The change in cyclin D1 mRNA level in MCF-7 cells recovered from K₃EDAT tube was minimal after 4 days incubation at room temperature.

In the example with results shown at FIG. 1 , 2000 MCF-7 cells were spiked into each K₃EDTA tube and tubes containing Protective Agent Compositions A & B and shipped from Omaha Nebr. to Maryville, Tenn. by overnight shipping for analysis by the CellSearch™ System. Thus, this example represents a combination of transportation as well as storage effect on CTCs in blood samples. As shown in FIG. 1 , our CTC recovery study conducted using spiked MCF-7 cells and analyzed by CellSearch™ System provided evidence that Protective Agent Compositions A & B are able to preserve CTCs during transportation and storage at room temperature for up to 4 days. Previous studies using CellSearch™ System have shown that the recovery rate for MCF-7 cells shortly after blood draw is between 62-89%. Our results show that in tubes containing Protective Agent Compositions A & B, post shipping day 1 and day 4 recovery rates of 61% and 57% respectively. There was no statistically significant difference between these two values indicating that CTCs are stable in Protective Agent Compositions A & B for 4 days after shipping at room temperature. However in K₃EDTA tubes, CTC recovery rate was very low compared to Protective Agent Compositions A & B. In K₃EDTA tubes post shipping day 1 and day 4 recovery rates were 32% and 16% respectively. There was a statistically significant decrease in CTC recovery in K₃EDTA tube at day 1 and day 4 compared to Protective Agent. Compositions A & B. As shown in FIG. 2 , immunofluorescence staining of recovered CTCs for EpCAM and CK showed stability of these proteins in CTCs recovered from Protective Agent Compositions A & B 4 days after storage at room temperature.. However cells recovered from K₃EDTA tubes showed degrading EpCAM and CK proteins after 4 days at the same temperature. DAPI staining of cells showed stable nucleus and nuclear content in CTCs recovered from Protective Agent Compositions A & B whereas CTCs recovered from K₃EDTA tubes showed degrading nucleus and nuclear content (FIG. 2 ).

The molecular beacon example shows that both c-fos and cycling D1 mRNA are stable in Protective Agent Composition A at room for up to 4 days (FIG. 3 ). However, CTCs recovered from K₃EDTA tubes showed CTCs with degrading c-fos and cyclin D1 mRNAs as shown in FIG. 3 .

Analysis of the stabilizing reagent present in Protective Agent Compositions A & B by ¹³C-NMR has shown that the reagent is free of formaldehyde. Aldehyde based chemicals traditionally used in cell stabilization, such as formaldehyde and glutaraldehyde, are known to damage DNA and RNA by causing chemical modifications in nucleic acids and making nucleic acid-protein cross-links which make extraction of nucleic acids difficult. Application of such aldehyde based chemicals for CTC stabilization may cause problems for CTC characterization studies. Cell stabilizing reagent present in Protective Agent Compositions A & B have an advantage over aldehyde based stabilizing agents because of it has no negative effect on either nucleic acid extraction or amplification by PCR.

In these examples, Protective Agent Compositions A & B provide preservation and stabilization of CTCs in blood samples for up to 4 days at room temperature. In doing so, the protective agent compositions support the development of new non-invasive diagnostic and prognostic methodologies for CTC enumeration as well as characterization.

The teachings herein envision that a single protective agent composition may be employed that includes a preservative composition and a quenching agent. Such protective agent composition may be preloaded into a sample collection device, such as a blood collection tube (which may be evacuated to a pressure below atmospheric pressure after loading). Thus, it is possible that a sample may be taken from a subject directly into the sample collection device (e.g., a blood collection tube), at which time it will be contacted with the protective agent composition. It is also possible that a sample can be taken from a subject into a first container and the sample subsequently transferred to one or more second containers in which the protective agent composition is present.

The aldehyde-free (e.g., formaldehyde-free) protective agent composition may include a preservative composition such as one selected from the group consisting of: diazolidinyl urea, imidazolidinyl urea, dimethoylol-5,5-dimethylhydantoin, diethyl urea, 2-bromo-2-nitropropane-1,3-diol, oxazolidines, sodium hydroxymethyl glycinate, 5-hydroxymethoxymethyl-1-laza-3,7-dioxabicyclo [3.3.0] octane, 5-hydroxymethyl-1-laza-3,7-dioxabicyclo [3.3.0] octane, 5-hydroxypoly[methyleneoxy]methyl-1-laza-3,7-dioxabicyclo [3.3.0] octane, quaternary adamantine and any combination thereof. Though the aldehyde-free (e.g., formaldehyde-free) protective agent composition may release an aldehyde (e.g., formaldehyde), the teachings herein envision a specific step of quenching the aldehyde to render it inert to the CTCs.

The preservative composition is desirably used in combination with a quenching agent for helping to assure that nucleic acid (e.g., DNA) in the sample avoids being subjected to free aldehyde (e.g., free formaldehyde) which may cause one or more deleterious effects upon the nucleic acid. Accordingly, the teachings herein contemplate the use of at least one aldehyde quenching agent, which is employed in an amount and in a manner sufficient so that any free aldehyde (e.g., formaldehyde) released from the protective agent composition reacts to form a reaction product that is inert to the nucleic acid of the biological sample. Further, the resulting mixture is preferably devoid of any aldehyde, and nucleic acids within the sample are suitable for polymerase chain reaction and DNA sequencing, and will exhibit structural integrity comparable to native nucleic acids (e.g., DNA will exhibit ellipticity that is substantially similar that of untreated native DNA, as measured by circular dichroism spectroscopy or will exhibit DNA-dye fluorescence that is substantially similar to that of untreated native DNA, as measured by fluorescence spectroscopy).

The concentration of the preservative composition after sample contact may be greater than about 20 mg/ml, 10 mg/ml, 5 mg/ml, 2 mg/ml, less than about 0.8 g/ml of the mixture of protective agent composition and biological (e.g., blood) sample. The concentration of the preservative composition after sample contact may be more than about 0.1 g/ml of the mixture of protective agent composition and biological (e.g., blood) sample. By way of example, the concentration of the preservative composition after sample contact may be between approximately 0.1 g/ml to approximately 0.8 g/ml of the mixture of protective agent composition and biological (e.g., blood) sample, The concentration of the preservative composition after sample contact may be between approximately 0.3 g/ml to approximately 0.6 g/ml of the mixture of protective agent composition and biological (e.g., blood) sample. The concentration of the preservative composition both before and after contact with a blood sample may be modified depending upon what diagnostic procedures a sample may undergo. As an example, the concentration may be modified in the event that a sample is to undergo flow cytometry analysis. More specifically, the concentration may be increased in the event that a sample is to undergo flow cytometry analysis. Thus, the concentration of the preservative composition after sample contact may be greater than about 15 mg/ml, greater than about 25 mg/ml, or even greater than about 30 mg/ml after sample contact. The formulation of the protective agent composition (and the preservative composition contained therein) may also be modified such that a sample that will undergo flow cytometry analysis may contain diazolidinyl urea. The protective agent composition may also include a quenching agent. The protective agent composition may also include one or more metabolic inhibitors, one or more nuclease inhibitors and EDTA.

The quenching agent may be one or more compounds that include at least one functional group capable of reacting with an electron deficient functional group of an aldehyde (e.g., an amine compound that reacts with formaldehyde to form methylol and/or imine Schiff base or a cis-diol compound that reacts with formaldehyde to form a cyclic acetal). The quenching agent may be selected from amino acids, alkyl amines, polyamines, primary amines, secondary amines, ammonium salts, nucleobases or any combination thereof. The quenching agent may be selected from glycine, lysine, ethylene diamine, arginine, urea, adinine, guanine, cytosine, thymine, spermidine, or any combination thereof.

The concentration of the quenching agent is an amount that is sufficiently large that after contacting the sample with the protective agent composition, there is an absence of free aldehyde (e.g., an absence of free formaldehyde). However, the concentration is sufficiently small that dilution of the sample will not materially impact any analyzed characteristic of the sample. The concentration of the formaldehyde-quenching reagent after the sample contacting step may be above about 0.001 g/ml, 0.002 g/ml or even about 0.004 ml of the mixture of protective agent composition and biological (e.g., blood) sample. The concentration of the formaldehyde-quenching reagent after the sample contacting step may be below about 0.03 g/ml, 0.01 g/ml, or even about 0.008 g/ml of the mixture of protective agent composition and biological (e.g., blood) sample. By way of example, the concentration of the formaldehyde-quenching reagent after the sample contacting step may be between about 0.004 g/ml to about 0.008 g/ml,

Upon being brought into contact with a sample to form a mixture of the sample and protective agent composition (e.g., at time of a blood draw into a blood collection device containing a protective agent composition of the teachings herein), the protective agent composition may be present in an overall small fraction of the mixture volume. For example, it may be present in an amount that is less than about 5%, 2%, 0.5% or even less than about 0.3% of the overall mixture volume. For example, the protective agent composition may be present in an amount of from about 1:20 parts by volume to about 1:300 parts by volume of the mixture. The amount of the protective agent composition may be present from about 1:50 parts by volume to about 1:200 parts by volume of the mixture.

During at least the contacting step, the amount of the protective agent composition is present from about 1:20 (1 part protective agent composition to 20 parts total mixture) parts by volume to about 1:300 parts by volume of the total mixture (which includes both the protective agent composition and the biological sample). For instance, during at least the contacting step, the amount of the protective agent composition is present from about 1:100 parts by volume to about 1:200 parts by volume of the mixture.

The protective agent composition may include at least one preservative composition selected from diazolidinyl urea, imidazolidinyl urea, dimethoylol-5,5-dimethylhydantoin, dimethylol urea, 2-bromo-2-nitropropane-1,3-diol, oxazolidines, sodium hydroxymethyl glycinate, 5-hydroxymethoxymethyl-1- laza-3,7-dioxabicyclo[3.3.0]actane, 5-hydroxymethyl-1-laza-3,7dioxabicyclo[3.3.0]octane, 5-hydroxypoly[methyleneoxy]methyl-1-laza-3,7 dioxabicyclo[3. 3.0]octane, quaternary adamantine, 2-aminoacetic acid or any combination thereof. By way of illustration, the contacting step may include employing as the protective agent composition, a composition that includes imidazolidinyl urea in an amount of about 0.1 to about 2.0% by weight of the total mixture of the protective agent composition plus a biological sample; optionally, ethylenediaminetetraacetic acid (EDTA) in an amount of about 0.05 to about 0.75% by weight of the total mixture of the protective agent composition plus a biological sample; and a quenching agent in an amount sufficient to react with any free aldehyde (e.g., formaldehyde) that may arise from the imidazolidinyl urea to form a reaction product that will not react to denature any protein of the biological sample. The protective agent composition (prior to contact with any biological sample) may include from about 20% to about 60% by weight imidazolidinyl urea. The protective agent composition may include at least about 30% by weight imidazolidinyl urea. The protective agent composition may include at least about 40% by weight imidazolidinyl urea and less than about 55% by weight imidazolidinyl urea. The protective agent composition may include from about 1% to about 10% by weight of the quenching agent. The protective agent composition may include at least about 2% by weight of the quenching agent. The protective agent composition may include at least about 4% by weight of the quenching agent and less than about 8% by weight of the quenching agent. The protective agent composition may include from about 1% to about 20% by weight EDTA. The protective agent composition may include at least about 5% by weight EDTA. The protective agent composition may include at least about 7% by weight EDTA and less than about 10% by weight EDTA.

The protective agent composition may be pre-loaded into a tube and may be pre-loaded in amount of from about 50 to about 400 μl of protective agent composition. The pre-loaded amount may be at least about 100 μl and less than about 300 μl. The pre-loaded amount may be at least about 150 μl and less than about 250 μl. Within the pre-loaded protective agent composition, the protective agent composition may comprise at least about 80 mg and less than about 100 mg of the protective agent composition. The quenching agent may comprise at least about 1 mg and less than about 15 mg of the protective agent composition. EDTA may comprise at least about 10 rng and less than about 25 mg of the protective agent composition. For the protective agent composition, it may include an amount of about 10 parts by weight of the protective agent composition per about 1 parts by weight of the quenching agent. The quenching agent may include a compound that includes at least one functional group capable of reacting with an electron deficient functional group of formaldehyde (e.g., an amine compound that reacts with formaldehyde to form methylol or imine Schiff base or a cis-diol compound that reacts with formaldehyde to form a cyclic acetal). The quenching agent may be an ingredient selected from amino acids, alkyl amines, polyamines, primary amines, secondary amines, ammonium salts, or a combination thereof, it may be an ingredient selected from glycine, lysine, ethylene diamine, arginine, urea, adinine, guanine, cytosine, thymine, spermidine, or any combination thereof. It may be an ingredient selected from glycine, lysine, ethylene diamine, urea or any combination thereof. The quenching step may include reacting any free aldehyde (e.g., formaldehyde) for forming a methylol, imine Schiff base, a Schiff base-quencher crosslink reaction product, a Schiff base dimer, or any combination thereof.

The protective agent may include one or more preservative agents, one or more nuclease inhibitors, one or more metabolic inhibitors, or any combination thereof. The one or more nuclease inhibitors may be selected from the group consisting of: diethyl pyrocarbonate, ethanol, aurintricarboxylic acid (ATA), glyceraldehydes, sodium fluoride, ethylenediamine tetraacetic acid (EDTA), formamide, vanadyl-ribonucleoside complexes, macaloid, heparin, hydroxylamine-oxygen-cupric ion, bentonite, ammonium sulfate, dithiothreitol (DTT), beta-mercaptoethanol, cysteine, dithioerythritol, tris (2-carboxyethyl) phosphene hydrochloride, a divalent cation such as Mg⁺², Zn⁺², Fe⁺², Ca⁺², Cu⁺² and any combination thereof. The one or more metabolic inhibitors may be selected from the group consisting of: glyceraldehyde, dihydroxyacetone phosphate, dyceraidehyde 3-phosphate, 1,3-bisphosphognlycerate, 3-phosphoglycerate, 2-phosphoglycerate, phosphoanolpyruvate, pyruvate and glycerate dihydroxyacetate, sodium fluoride, K₂C₂O₄ and any combination thereof.

The amount of any active ingredient within the protective agent may generally be at least about 0.01% by weight. The amount of any active ingredient within the protective agent may generally be less than about 70% by weight. The protective agent may comprise at least about 10% diazolidinyl urea. The protective agent may comprise less than about 40% diazolidinyl urea. The protective agent may further contain at least about 1% of one or more enzyme inhibitors (e.g., nuclease inhibitors) such as EDTA and ATA. The protective agent may contain less than about 30% of one or more enzyme inhibitors. The protective agent may also contain at least about 1% of one or more metabolic inhibitors. The protective agent may contain less than about 20% of one or more metabolic inhibitors.

The protective agent composition optionally may include a nuclease inhibitor selected from the group consisting of: diethyl pyrocarbonate, ethanol, aurintricarboxylic acid (ATA), formamide, vanadyl-ribonucleoside complexes, macaloid, ethylenediamine tetraacetic acid (EDTA), proteinase K, heparin, hydroxylamine-oxygen-cupric ion, bentonite, ammonium sulfate, dithiothreitol (DTT), beta-mercaptoethanol (BME), cysteine, dithioerythritol, tris(2-carboxyethyl) phosphene hydrochloride, a divalent cation such as Mg²⁺, Mn²⁺, Zn²⁺, Fe²⁺, Ca²⁺, Cu²⁺, and any combination thereof. The protective agent composition may include a preservative composition, an aldehyde quenching agent, and an anticoagulant. In one preferred embodiment, the protective agent composition may include imidazolidinyl urea, glycine, and ethylenediamine tetraacetic acid,

The teachings herein contemplate applications including but not limited to extracting circulating tumor cells for use in detecting cancer (including but not limited to carcinomas, leukemia, and/or lymphoma). For instance, the teachings herein may be employed for detecting abnormal methylation for breast cancer, prostate cancer, gastric cancer, ovarian, colorectal cancer, bladder cancer, testicular cancer, esophogeal cancer, melanoma or other cancers.

The explanations and illustrations presented herein are intended to acquaint others skilled in the art with the invention, its principles, and its practical application. Those skilled in the art may adapt and apply the invention in its numerous forms, as may be best suited to the requirements of a particular use. Accordingly, the specific embodiments of the present invention as set forth are not intended as being exhaustive or limiting of the invention. The scope of the invention should, therefore, be determined not only with reference to the above description, but should instead be determined with reference to the appended claims, along with the full scope of equivalents to which such claims are entitled. The disclosures of all articles and references, including patent applications and publications, are incorporated by reference for all purposes. Other combinations are also possible as will be gleaned from the following claims, which are also hereby incorporated by reference into this written description. As to all of the foregoing general teachings, as used herein, unless otherwise stated, the teachings envision that any member of a genus (list) may be excluded from the genus; and/or any member of a Markush grouping may be excluded from the grouping.

Unless otherwise stated, any numerical values recited herein include all values from the lower value to the upper value in increments of one unit provided that there is a separation of at least 2 units between any lower value and any higher value. As an example, if it is stated that the amount of a component, a property, or a value of a process variable such as, for example, temperature, pressure, time and the like is, for example, from 1 to 90, preferably from 20 to 80, more preferably from 30 to 70, it is intended that intermediate range values (for example, 15 to 85, 22 to 68, 43 to 51, 30 to 32 etc.) are within the teachings of this specification. Likewise, individual intermediate values are also within the present teachings. For values which are less than one, one unit is considered to be 0.0001, 0.001, 0.01 or 0.1 as appropriate. These are only examples of what is specifically intended and all possible combinations of numerical values between the lowest value and the highest value enumerated are to be considered to be expressly stated in this application in a similar manner. As can be seen, the teaching of amounts expressed as “parts by weight” herein also contemplates the same ranges expressed in terms of percent by weight and vice versa. Thus, an expression in the Detailed Description of the Invention of a range in terms of at “x” parts by weight of the resulting polymeric blend composition” also contemplates a teaching of ranges of same recited amount of “x” in percent by weight of the resulting polymeric blend composition.”

Unless otherwise stated, all ranges include both endpoints and all numbers between the endpoints, The use of “about” or “approximately” in connection with a range applies to both ends of the range. Thus, “about 20 to 30” is intended to cover “about 20 to about 30”, inclusive of at least the specified endpoints. Concentrations of ingredients identified in Tables herein may vary ±10%, or even 20% or more and remain within the teachings.

The disclosures of all articles and references, including patent applications and publications, are incorporated by reference for all purposes. The term “consisting essentially of” to describe a combination shall include the elements, ingredients, components or steps identified, and such other elements ingredients, components or steps that do not materially affect the basic and novel characteristics of the combination. The use of the terms “comprising” or “including” to describe combinations of elements, ingredients, components or steps herein also contemplates embodiments that consist essentially of, or even consist of the elements, ingredients, components or steps. Plural elements, ingredients, components or steps can be provided by a single integrated element, ingredient, component or step. Alternatively, a single integrated element, ingredient, component or step might be divided into separate plural elements, ingredients, components or steps. The disclosure of “a” or “one” to describe an element, ingredient, component or step is not intended to foreclose additional elements, ingredients, components or steps. All references herein to elements or metals belonging to a certain Group refer to the Periodic Table of the Elements published and copyrighted by CRC Press, Inc., 1989. Any reference to the Group or Groups shall be to the Group or Groups as reflected in this Periodic Table of the Elements using the IUPAC system for numbering groups.

Even if not expressly stated, teachings from a description of one embodiment may be combined with teachings for other embodiments unless the description makes clear that such embodiments are mutually exclusive, or that the resulting combination would be clearly inoperative in the absence of unreasonable experimentation.

It is understood that the above description is intended to be illustrative and not restrictive. Many embodiments as well as many applications besides the examples provided will be apparent to those of skill in the art upon reading the above description. The scope of the invention should, therefore, be determined not with reference to the above description, but should instead be determined with reference to the appended claims, along with the full scope of equivalents to which such claims are entitled. The disclosures of all articles and references, including patent applications and publications, are incorporated by reference for all purposes. The omission in the following claims of any aspect of subject matter that is disclosed herein is not a disclaimer of such subject matter, nor should it be regarded that the inventors did not consider such subject matter to be part of the disclosed inventive subject matter. 

1. A device comprising: an evacuated tube that includes: (i) a blood sample including one or more tumor-based nucleic acid fragments present within the blood sample in a first concentration; (ii) a protective agent in an amount of at least about 300 μl comprising a preservative composition selected from imidazolidinyl urea, diazolidinyl urea, or a combination thereof and an anticoagulant; wherein the preservative composition is present in an amount of from 10 mg/ml to 20 mg/ml of the total blood sample and protective agent and less than 60% by weight of the protective agent, and the anticoagulant being present in an amount of less than 10% by weight of the protective agent; and wherein at least 24 hours after contact between the protective agent and the blood sample, the one or more tumor-based nucleic acid fragments are present in a second concentration that is not lower or higher than the first concentration by any statistically significant value.
 2. The device of claim 1, wherein the preservative composition is diazolidinyl urea.
 3. (canceled)
 4. The device of claim 1, wherein the one or more tumor-based nucleic acid fragments are isolated from the sample at least 3 days after blood draw.
 5. The device of claim 1, wherein the one or more tumor-based nucleic acid fragments are isolated from the sample at least 7 days after blood draw.
 6. The device of claim 1, wherein the circulating tumor cells are isolated from the sample at least 14 days after blood draw.
 7. The device of claim 1, wherein blood sample is never frozen to a temperature colder than about −30° C. 8-9. (canceled)
 10. The device of claim 1, wherein the protective agent composition includes: a. imidazolidinyl urea in an amount of about 1.0% by weight of the total composition; ethylenediaminetetraacetic acid in an amount of about 0.05 to about 0.75% by weight of the total composition.
 11. The device of claim 1, wherein the protective agent composition includes a quenching agent.
 12. The device of claim 1, wherein there is no significant degradation of EpCAM proteins in the blood sample after 4 days at room temperature.
 13. The device of claim 7, wherein there is no significant degradation of CK proteins in the blood sample after 4 days at room temperature. 14-20. (canceled)
 21. The device of claim 1, wherein the protective agent comprises diethyl pyrocarbonate, ethanol, aurintricarboxylic acid (ATA), glyceraldehydes, sodium fluoride, ethylenediamine tetraacetic acid (EDTA), formamide, vanadyl-ribonucleoside complexes, macaloid, heparin, hydroxylamine-oxygen-cupric ion, bentonite, ammonium sulfate, dithiothreitol (DTT), beta-mercaptoethanol, cysteine, dithioerythritol, tris (2-carboxyethyl) phosphene hydrochloride, a divalent cation such as Mg+2, Mn+2, Zn+2, Fe+2, Ca+2, Cu+2, or any combination thereof.
 22. The device of claim 1, wherein the protective agent comprises dihydroxyacetone phosphate, glyceraldehyde 3-phosphate, 1,3-bisphosphoglycerate, 3-phosphoglycerate, 2-phosphoglycerate, phosphoenolpyruvate, pyruvate and glycerate dihydroxyacetate, sodium fluoride, K2C204, or any combination thereof.
 23. The device of claim 1, wherein DNA present in the treated blood samples exhibits ellipticity that is substantially similar to that of untreated native DNA as measured by circular dichroism spectroscopy.
 24. The device of claim 1, wherein DNA present in the treated blood samples exhibits DNA-dye fluorescence that is substantially similar to that of untreated native DNA as measured by fluorescence spectroscopy.
 25. The device of claim 7, wherein DNA present in the treated blood samples exhibits ellipticity that is substantially similar to that of untreated native DNA as measured by circular dichroism spectroscopy.
 26. The device of claim 7, wherein DNA present in the treated blood samples exhibits DNA-dye fluorescence that is substantially similar to that of untreated native DNA as measured by fluorescence spectroscopy.
 27. The device of claim 1, wherein protective agent includes beta-mercaptoethanol.
 28. The device of claim 1, wherein cyclin D1 mRNA levels in the blood sample remains stable after 4 days at room temperature.
 29. The device of claim 26, wherein cyclin D1 mRNA levels in the blood sample remains stable after 4 days at room temperature.
 30. A device comprising: an evacuated tube that includes: (i) a blood sample including one or more tumor-based nucleic acid fragments present within the blood sample in a first concentration; (ii) a protective agent in an amount of at least about 300 μl comprising a preservative composition selected from imidazolidinyl urea, diazolidinyl urea, or a combination thereof and an anticoagulant; wherein the preservative composition is present in an amount of from 10 mg/ml to 20 mg/ml of the total blood sample and protective agent and less than 60% by weight of the protective agent, and the anticoagulant being present in an amount of less than 10% by weight of the protective agent; wherein at least 24 hours after contact between the protective agent and the blood sample, the one or more tumor-based nucleic acid fragments are present in a second concentration that is not lower or higher than the first concentration by any statistically significant value; wherein there is no significant degradation of EpCAM proteins in the blood sample after 4 days at room temperature; and wherein there is no significant degradation of CK proteins in the blood sample after 4 days at room temperature. 